| aa_composition_setup_file(core::Size const index) const | core::scoring::methods::EnergyMethodOptions | inline |
| aa_composition_setup_file_count() const | core::scoring::methods::EnergyMethodOptions | inline |
| aa_composition_setup_files_ | core::scoring::methods::EnergyMethodOptions | private |
| analytic_etable_evaluation() const | core::scoring::methods::EnergyMethodOptions | |
| analytic_etable_evaluation(bool setting) | core::scoring::methods::EnergyMethodOptions | |
| append_aa_composition_setup_files(utility::vector1< std::string > const &input_filenames) | core::scoring::methods::EnergyMethodOptions | inline |
| append_mhc_epitope_setup_files(utility::vector1< std::string > const &input_filenames) | core::scoring::methods::EnergyMethodOptions | inline |
| append_netcharge_setup_files(utility::vector1< std::string > const &input_filenames) | core::scoring::methods::EnergyMethodOptions | inline |
| approximate_buried_unsat_penalty_assume_const_backbone(bool const setting) | core::scoring::methods::EnergyMethodOptions | |
| approximate_buried_unsat_penalty_assume_const_backbone() const | core::scoring::methods::EnergyMethodOptions | |
| approximate_buried_unsat_penalty_assume_const_backbone_ | core::scoring::methods::EnergyMethodOptions | private |
| approximate_buried_unsat_penalty_burial_atomic_depth(core::Real const setting) | core::scoring::methods::EnergyMethodOptions | |
| approximate_buried_unsat_penalty_burial_atomic_depth() const | core::scoring::methods::EnergyMethodOptions | |
| approximate_buried_unsat_penalty_burial_atomic_depth_ | core::scoring::methods::EnergyMethodOptions | private |
| approximate_buried_unsat_penalty_burial_probe_radius(core::Real const setting) | core::scoring::methods::EnergyMethodOptions | |
| approximate_buried_unsat_penalty_burial_probe_radius() const | core::scoring::methods::EnergyMethodOptions | |
| approximate_buried_unsat_penalty_burial_probe_radius_ | core::scoring::methods::EnergyMethodOptions | private |
| approximate_buried_unsat_penalty_burial_resolution(core::Real const setting) | core::scoring::methods::EnergyMethodOptions | |
| approximate_buried_unsat_penalty_burial_resolution() const | core::scoring::methods::EnergyMethodOptions | |
| approximate_buried_unsat_penalty_burial_resolution_ | core::scoring::methods::EnergyMethodOptions | private |
| approximate_buried_unsat_penalty_hbond_bonus_cross_chain(core::Real const setting) | core::scoring::methods::EnergyMethodOptions | |
| approximate_buried_unsat_penalty_hbond_bonus_cross_chain() const | core::scoring::methods::EnergyMethodOptions | |
| approximate_buried_unsat_penalty_hbond_bonus_cross_chain_ | core::scoring::methods::EnergyMethodOptions | private |
| approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb(core::Real const setting) | core::scoring::methods::EnergyMethodOptions | |
| approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb() const | core::scoring::methods::EnergyMethodOptions | |
| approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb_ | core::scoring::methods::EnergyMethodOptions | private |
| approximate_buried_unsat_penalty_hbond_energy_threshold(core::Real const setting) | core::scoring::methods::EnergyMethodOptions | |
| approximate_buried_unsat_penalty_hbond_energy_threshold() const | core::scoring::methods::EnergyMethodOptions | |
| approximate_buried_unsat_penalty_hbond_energy_threshold_ | core::scoring::methods::EnergyMethodOptions | private |
| approximate_buried_unsat_penalty_natural_corrections1(bool const setting) | core::scoring::methods::EnergyMethodOptions | |
| approximate_buried_unsat_penalty_natural_corrections1() const | core::scoring::methods::EnergyMethodOptions | |
| approximate_buried_unsat_penalty_natural_corrections1_ | core::scoring::methods::EnergyMethodOptions | private |
| approximate_buried_unsat_penalty_oversat_penalty(core::Real const setting) | core::scoring::methods::EnergyMethodOptions | |
| approximate_buried_unsat_penalty_oversat_penalty() const | core::scoring::methods::EnergyMethodOptions | |
| approximate_buried_unsat_penalty_oversat_penalty_ | core::scoring::methods::EnergyMethodOptions | private |
| arg_cation_pi_his_can_be_pi() const | core::scoring::methods::EnergyMethodOptions | |
| arg_cation_pi_his_can_be_pi(bool const setting) | core::scoring::methods::EnergyMethodOptions | |
| arg_cation_pi_his_can_be_pi_ | core::scoring::methods::EnergyMethodOptions | private |
| aspartimide_penalty_value() const | core::scoring::methods::EnergyMethodOptions | inline |
| aspartimide_penalty_value_ | core::scoring::methods::EnergyMethodOptions | private |
| atom_vdw_atom_type_set_name() const | core::scoring::methods::EnergyMethodOptions | |
| atom_vdw_atom_type_set_name(std::string const &setting) | core::scoring::methods::EnergyMethodOptions | |
| atom_vdw_atom_type_set_name_ | core::scoring::methods::EnergyMethodOptions | private |
| bond_angle_central_atoms_to_score() const | core::scoring::methods::EnergyMethodOptions | |
| bond_angle_central_atoms_to_score(utility::vector1< std::string > const &atom_names) | core::scoring::methods::EnergyMethodOptions | |
| bond_angle_central_atoms_to_score_ | core::scoring::methods::EnergyMethodOptions | private |
| bond_angle_residue_type_param_set() | core::scoring::methods::EnergyMethodOptions | |
| bond_angle_residue_type_param_set() const | core::scoring::methods::EnergyMethodOptions | |
| bond_angle_residue_type_param_set(scoring::mm::MMBondAngleResidueTypeParamSetOP param_set) | core::scoring::methods::EnergyMethodOptions | |
| bond_angle_residue_type_param_set_ | core::scoring::methods::EnergyMethodOptions | private |
| buried_unsatisfied_penalty_burial_threshold(core::Real const setting) | core::scoring::methods::EnergyMethodOptions | |
| buried_unsatisfied_penalty_burial_threshold() const | core::scoring::methods::EnergyMethodOptions | |
| buried_unsatisfied_penalty_burial_threshold_ | core::scoring::methods::EnergyMethodOptions | private |
| buried_unsatisfied_penalty_cone_angle_exponent(core::Real const setting) | core::scoring::methods::EnergyMethodOptions | |
| buried_unsatisfied_penalty_cone_angle_exponent() const | core::scoring::methods::EnergyMethodOptions | |
| buried_unsatisfied_penalty_cone_angle_exponent_ | core::scoring::methods::EnergyMethodOptions | private |
| buried_unsatisfied_penalty_cone_angle_shift_factor(core::Real const setting) | core::scoring::methods::EnergyMethodOptions | |
| buried_unsatisfied_penalty_cone_angle_shift_factor() const | core::scoring::methods::EnergyMethodOptions | |
| buried_unsatisfied_penalty_cone_angle_shift_factor_ | core::scoring::methods::EnergyMethodOptions | private |
| buried_unsatisfied_penalty_cone_dist_exponent(core::Real const setting) | core::scoring::methods::EnergyMethodOptions | |
| buried_unsatisfied_penalty_cone_dist_exponent() const | core::scoring::methods::EnergyMethodOptions | |
| buried_unsatisfied_penalty_cone_dist_exponent_ | core::scoring::methods::EnergyMethodOptions | private |
| buried_unsatisfied_penalty_cone_dist_midpoint(core::Real const setting) | core::scoring::methods::EnergyMethodOptions | |
| buried_unsatisfied_penalty_cone_dist_midpoint() const | core::scoring::methods::EnergyMethodOptions | |
| buried_unsatisfied_penalty_cone_dist_midpoint_ | core::scoring::methods::EnergyMethodOptions | private |
| buried_unsatisfied_penalty_hbond_energy_threshold(core::Real const setting) | core::scoring::methods::EnergyMethodOptions | |
| buried_unsatisfied_penalty_hbond_energy_threshold() const | core::scoring::methods::EnergyMethodOptions | |
| buried_unsatisfied_penalty_hbond_energy_threshold_ | core::scoring::methods::EnergyMethodOptions | private |
| cartbonded_ang_ | core::scoring::methods::EnergyMethodOptions | private |
| cartbonded_improper_ | core::scoring::methods::EnergyMethodOptions | private |
| cartbonded_len_ | core::scoring::methods::EnergyMethodOptions | private |
| cartbonded_linear_ | core::scoring::methods::EnergyMethodOptions | private |
| cartbonded_proton_ | core::scoring::methods::EnergyMethodOptions | private |
| cartbonded_skip_cutpoints_ | core::scoring::methods::EnergyMethodOptions | private |
| cartbonded_tors_ | core::scoring::methods::EnergyMethodOptions | private |
| clone() const | core::scoring::methods::EnergyMethodOptions | inline |
| count_pair_full() const | core::scoring::methods::EnergyMethodOptions | |
| count_pair_full(bool const setting) | core::scoring::methods::EnergyMethodOptions | |
| count_pair_full_ | core::scoring::methods::EnergyMethodOptions | private |
| count_pair_hybrid() const | core::scoring::methods::EnergyMethodOptions | |
| count_pair_hybrid(bool const setting) | core::scoring::methods::EnergyMethodOptions | |
| count_pair_hybrid_ | core::scoring::methods::EnergyMethodOptions | private |
| covalent_labeling_fa_input() const | core::scoring::methods::EnergyMethodOptions | |
| covalent_labeling_fa_input(std::string const &setting) | core::scoring::methods::EnergyMethodOptions | |
| covalent_labeling_fa_input_ | core::scoring::methods::EnergyMethodOptions | private |
| covalent_labeling_input() const | core::scoring::methods::EnergyMethodOptions | |
| covalent_labeling_input(std::string const &setting) | core::scoring::methods::EnergyMethodOptions | |
| covalent_labeling_input_ | core::scoring::methods::EnergyMethodOptions | private |
| cst_max_seq_sep() const | core::scoring::methods::EnergyMethodOptions | |
| cst_max_seq_sep(Size const setting) | core::scoring::methods::EnergyMethodOptions | |
| cst_max_seq_sep_ | core::scoring::methods::EnergyMethodOptions | private |
| dump_trajectory_gz(bool const setting) | core::scoring::methods::EnergyMethodOptions | |
| dump_trajectory_gz() const | core::scoring::methods::EnergyMethodOptions | inline |
| dump_trajectory_gz_ | core::scoring::methods::EnergyMethodOptions | private |
| dump_trajectory_prefix(std::string const &setting) | core::scoring::methods::EnergyMethodOptions | |
| dump_trajectory_prefix() const | core::scoring::methods::EnergyMethodOptions | inline |
| dump_trajectory_prefix_ | core::scoring::methods::EnergyMethodOptions | private |
| dump_trajectory_stride(signed long int setting) | core::scoring::methods::EnergyMethodOptions | |
| dump_trajectory_stride() const | core::scoring::methods::EnergyMethodOptions | inline |
| dump_trajectory_stride_ | core::scoring::methods::EnergyMethodOptions | private |
| elec_die() const | core::scoring::methods::EnergyMethodOptions | |
| elec_die(core::Real setting) | core::scoring::methods::EnergyMethodOptions | |
| elec_die_ | core::scoring::methods::EnergyMethodOptions | private |
| elec_group_file() const | core::scoring::methods::EnergyMethodOptions | |
| elec_group_file(std::string setting) | core::scoring::methods::EnergyMethodOptions | |
| elec_group_file_ | core::scoring::methods::EnergyMethodOptions | private |
| elec_max_dis() const | core::scoring::methods::EnergyMethodOptions | |
| elec_max_dis(core::Real setting) | core::scoring::methods::EnergyMethodOptions | |
| elec_max_dis_ | core::scoring::methods::EnergyMethodOptions | private |
| elec_min_dis() const | core::scoring::methods::EnergyMethodOptions | |
| elec_min_dis(core::Real setting) | core::scoring::methods::EnergyMethodOptions | |
| elec_min_dis_ | core::scoring::methods::EnergyMethodOptions | private |
| elec_no_dis_dep_die() const | core::scoring::methods::EnergyMethodOptions | |
| elec_no_dis_dep_die(bool setting) | core::scoring::methods::EnergyMethodOptions | |
| elec_no_dis_dep_die_ | core::scoring::methods::EnergyMethodOptions | private |
| elec_sigmoidal_D0_ | core::scoring::methods::EnergyMethodOptions | private |
| elec_sigmoidal_D_ | core::scoring::methods::EnergyMethodOptions | private |
| elec_sigmoidal_die() const | core::scoring::methods::EnergyMethodOptions | |
| elec_sigmoidal_die(bool const setting) | core::scoring::methods::EnergyMethodOptions | |
| elec_sigmoidal_die_ | core::scoring::methods::EnergyMethodOptions | private |
| elec_sigmoidal_die_params(Real &D, Real &D0, Real &S) const | core::scoring::methods::EnergyMethodOptions | |
| elec_sigmoidal_S_ | core::scoring::methods::EnergyMethodOptions | private |
| EnergyMethodOptions() | core::scoring::methods::EnergyMethodOptions | |
| EnergyMethodOptions(utility::options::OptionCollection const &options) | core::scoring::methods::EnergyMethodOptions | |
| EnergyMethodOptions(EnergyMethodOptions const &src) | core::scoring::methods::EnergyMethodOptions | |
| envsmooth_zero_negatives() const | core::scoring::methods::EnergyMethodOptions | |
| envsmooth_zero_negatives(bool const setting) | core::scoring::methods::EnergyMethodOptions | |
| envsmooth_zero_negatives_ | core::scoring::methods::EnergyMethodOptions | private |
| etable_options() const | core::scoring::methods::EnergyMethodOptions | |
| etable_options() | core::scoring::methods::EnergyMethodOptions | |
| etable_options(etable::EtableOptions const &opts) | core::scoring::methods::EnergyMethodOptions | |
| etable_options_ | core::scoring::methods::EnergyMethodOptions | private |
| etable_type() const | core::scoring::methods::EnergyMethodOptions | |
| etable_type(std::string const &type) | core::scoring::methods::EnergyMethodOptions | |
| eval_intrares_elec_ST_only() const | core::scoring::methods::EnergyMethodOptions | |
| eval_intrares_elec_ST_only_ | core::scoring::methods::EnergyMethodOptions | private |
| eval_intrsres_elec_ST_only(bool setting) | core::scoring::methods::EnergyMethodOptions | |
| exclude_DNA_DNA() const | core::scoring::methods::EnergyMethodOptions | |
| exclude_DNA_DNA(bool const setting) | core::scoring::methods::EnergyMethodOptions | |
| exclude_DNA_DNA_ | core::scoring::methods::EnergyMethodOptions | private |
| exclude_intra_res_protein() const | core::scoring::methods::EnergyMethodOptions | |
| exclude_intra_res_protein(bool const setting) | core::scoring::methods::EnergyMethodOptions | |
| exclude_intra_res_protein_ | core::scoring::methods::EnergyMethodOptions | private |
| exclude_monomer_fa_elec() const | core::scoring::methods::EnergyMethodOptions | |
| exclude_monomer_fa_elec(bool const setting) | core::scoring::methods::EnergyMethodOptions | |
| exclude_monomer_fa_elec_ | core::scoring::methods::EnergyMethodOptions | private |
| exclude_protein_protein_fa_elec() const | core::scoring::methods::EnergyMethodOptions | |
| exclude_protein_protein_fa_elec(bool const setting) | core::scoring::methods::EnergyMethodOptions | |
| exclude_protein_protein_fa_elec_ | core::scoring::methods::EnergyMethodOptions | private |
| exclude_RNA_protein_fa_elec() const | core::scoring::methods::EnergyMethodOptions | |
| exclude_RNA_protein_fa_elec(bool const setting) | core::scoring::methods::EnergyMethodOptions | |
| exclude_RNA_protein_fa_elec_ | core::scoring::methods::EnergyMethodOptions | private |
| exclude_RNA_RNA_fa_elec() const | core::scoring::methods::EnergyMethodOptions | |
| exclude_RNA_RNA_fa_elec(bool const setting) | core::scoring::methods::EnergyMethodOptions | |
| exclude_RNA_RNA_fa_elec_ | core::scoring::methods::EnergyMethodOptions | private |
| fa_stack_base_all() const | core::scoring::methods::EnergyMethodOptions | |
| fa_stack_base_all(bool const setting) | core::scoring::methods::EnergyMethodOptions | |
| fa_stack_base_all_ | core::scoring::methods::EnergyMethodOptions | private |
| fastdens_perres_weights_ | core::scoring::methods::EnergyMethodOptions | private |
| free_dof_options() const | core::scoring::methods::EnergyMethodOptions | |
| free_dof_options() | core::scoring::methods::EnergyMethodOptions | |
| free_dof_options(methods::FreeDOF_Options const &opts) | core::scoring::methods::EnergyMethodOptions | |
| free_dof_options_ | core::scoring::methods::EnergyMethodOptions | private |
| genbonded_score_full() const | core::scoring::methods::EnergyMethodOptions | inline |
| genbonded_score_full(bool setting) | core::scoring::methods::EnergyMethodOptions | inline |
| genbonded_score_full_ | core::scoring::methods::EnergyMethodOptions | private |
| genbonded_score_hybrid() const | core::scoring::methods::EnergyMethodOptions | inline |
| genbonded_score_hybrid(bool setting) | core::scoring::methods::EnergyMethodOptions | inline |
| genbonded_score_hybrid_ | core::scoring::methods::EnergyMethodOptions | private |
| geom_sol_interres_path_distance_cutoff() const | core::scoring::methods::EnergyMethodOptions | |
| geom_sol_interres_path_distance_cutoff(core::Size const setting) | core::scoring::methods::EnergyMethodOptions | |
| geom_sol_interres_path_distance_cutoff_ | core::scoring::methods::EnergyMethodOptions | private |
| geom_sol_intrares_path_distance_cutoff() const | core::scoring::methods::EnergyMethodOptions | |
| geom_sol_intrares_path_distance_cutoff(core::Size const setting) | core::scoring::methods::EnergyMethodOptions | |
| geom_sol_intrares_path_distance_cutoff_ | core::scoring::methods::EnergyMethodOptions | private |
| get_cartesian_bonded_linear() const | core::scoring::methods::EnergyMethodOptions | inline |
| get_cartesian_bonded_parameters(Real &len, Real &ang, Real &tors, Real &proton, Real &imp) const | core::scoring::methods::EnergyMethodOptions | inline |
| get_cartesian_bonded_skip_cutpoints() const | core::scoring::methods::EnergyMethodOptions | inline |
| get_density_sc_scale_byres() const | core::scoring::methods::EnergyMethodOptions | |
| grp_cpfxn() const | core::scoring::methods::EnergyMethodOptions | |
| grp_cpfxn(bool setting) | core::scoring::methods::EnergyMethodOptions | |
| grp_cpfxn_ | core::scoring::methods::EnergyMethodOptions | private |
| grpelec_context_dependent() const | core::scoring::methods::EnergyMethodOptions | |
| grpelec_context_dependent(bool setting) | core::scoring::methods::EnergyMethodOptions | |
| grpelec_context_dependent_ | core::scoring::methods::EnergyMethodOptions | private |
| grpelec_fade_hbond() const | core::scoring::methods::EnergyMethodOptions | |
| grpelec_fade_hbond(bool setting) | core::scoring::methods::EnergyMethodOptions | |
| grpelec_fade_hbond_ | core::scoring::methods::EnergyMethodOptions | private |
| grpelec_fade_param1() const | core::scoring::methods::EnergyMethodOptions | |
| grpelec_fade_param1(core::Real setting) | core::scoring::methods::EnergyMethodOptions | |
| grpelec_fade_param1_ | core::scoring::methods::EnergyMethodOptions | private |
| grpelec_fade_param2() const | core::scoring::methods::EnergyMethodOptions | |
| grpelec_fade_param2(core::Real setting) | core::scoring::methods::EnergyMethodOptions | |
| grpelec_fade_param2_ | core::scoring::methods::EnergyMethodOptions | private |
| grpelec_fade_type() const | core::scoring::methods::EnergyMethodOptions | |
| grpelec_fade_type(std::string setting) | core::scoring::methods::EnergyMethodOptions | |
| grpelec_fade_type_ | core::scoring::methods::EnergyMethodOptions | private |
| has_method_weights(ScoreType const &type) const | core::scoring::methods::EnergyMethodOptions | |
| hb_cen_soft(bool const setting) | core::scoring::methods::EnergyMethodOptions | |
| hb_cen_soft() const | core::scoring::methods::EnergyMethodOptions | |
| hb_cen_soft_ | core::scoring::methods::EnergyMethodOptions | private |
| hbnet_bonus_function_ramping() const | core::scoring::methods::EnergyMethodOptions | |
| hbnet_bonus_function_ramping(std::string const &setting) | core::scoring::methods::EnergyMethodOptions | |
| hbnet_bonus_ramping_function_ | core::scoring::methods::EnergyMethodOptions | private |
| hbnet_max_network_size() const | core::scoring::methods::EnergyMethodOptions | |
| hbnet_max_network_size(core::Size const setting) | core::scoring::methods::EnergyMethodOptions | |
| hbnet_max_network_size_ | core::scoring::methods::EnergyMethodOptions | private |
| hbond_options() const | core::scoring::methods::EnergyMethodOptions | |
| hbond_options() | core::scoring::methods::EnergyMethodOptions | |
| hbond_options(hbonds::HBondOptions const &opts) | core::scoring::methods::EnergyMethodOptions | |
| hbond_options_ | core::scoring::methods::EnergyMethodOptions | private |
| hrf_dynamics_input() const | core::scoring::methods::EnergyMethodOptions | |
| hrf_dynamics_input(std::string const &setting) | core::scoring::methods::EnergyMethodOptions | |
| hrf_dynamics_input_ | core::scoring::methods::EnergyMethodOptions | private |
| initialize_from_options() | core::scoring::methods::EnergyMethodOptions | |
| initialize_from_options(utility::options::OptionCollection const &options) | core::scoring::methods::EnergyMethodOptions | |
| insert_score_function_method_options_rows(Size batch_id, std::string const &score_function_name, utility::sql_database::sessionOP db_session) const | core::scoring::methods::EnergyMethodOptions | |
| list_options_read(utility::options::OptionKeyList &read_options) | core::scoring::methods::EnergyMethodOptions | static |
| loop_close_use_6D_potential() const | core::scoring::methods::EnergyMethodOptions | |
| loop_close_use_6D_potential(bool const setting) | core::scoring::methods::EnergyMethodOptions | |
| loop_close_use_6D_potential_ | core::scoring::methods::EnergyMethodOptions | private |
| method_weights(ScoreType const &type) const | core::scoring::methods::EnergyMethodOptions | |
| method_weights_ | core::scoring::methods::EnergyMethodOptions | private |
| MethodWeights typedef | core::scoring::methods::EnergyMethodOptions | private |
| mhc_epitope_setup_file(core::Size const index) const | core::scoring::methods::EnergyMethodOptions | inline |
| mhc_epitope_setup_file_count() const | core::scoring::methods::EnergyMethodOptions | inline |
| mhc_epitope_setup_files_ | core::scoring::methods::EnergyMethodOptions | private |
| netcharge_setup_file(core::Size const index) const | core::scoring::methods::EnergyMethodOptions | inline |
| netcharge_setup_file_count() const | core::scoring::methods::EnergyMethodOptions | inline |
| netcharge_setup_files_ | core::scoring::methods::EnergyMethodOptions | private |
| nmer_ref_seq_length() const | core::scoring::methods::EnergyMethodOptions | |
| nmer_ref_seq_length(core::Size const setting) | core::scoring::methods::EnergyMethodOptions | |
| nmer_ref_seq_length_ | core::scoring::methods::EnergyMethodOptions | private |
| nmer_svm() const | core::scoring::methods::EnergyMethodOptions | |
| nmer_svm(std::string const &filename) | core::scoring::methods::EnergyMethodOptions | |
| nmer_svm_ | core::scoring::methods::EnergyMethodOptions | private |
| nmer_svm_aa_matrix() const | core::scoring::methods::EnergyMethodOptions | |
| nmer_svm_aa_matrix(std::string const &filename) | core::scoring::methods::EnergyMethodOptions | |
| nmer_svm_aa_matrix_ | core::scoring::methods::EnergyMethodOptions | private |
| nmer_svm_aa_matrix_defined() const | core::scoring::methods::EnergyMethodOptions | |
| nmer_svm_aa_matrix_defined_ | core::scoring::methods::EnergyMethodOptions | private |
| nmer_svm_avg_rank_as_energy() const | core::scoring::methods::EnergyMethodOptions | |
| nmer_svm_avg_rank_as_energy(bool const setting) | core::scoring::methods::EnergyMethodOptions | |
| nmer_svm_avg_rank_as_energy_ | core::scoring::methods::EnergyMethodOptions | private |
| nmer_svm_defined() const | core::scoring::methods::EnergyMethodOptions | |
| nmer_svm_defined_ | core::scoring::methods::EnergyMethodOptions | private |
| nmer_svm_list() const | core::scoring::methods::EnergyMethodOptions | |
| nmer_svm_list(std::string const &filename) | core::scoring::methods::EnergyMethodOptions | |
| nmer_svm_list_ | core::scoring::methods::EnergyMethodOptions | private |
| nmer_svm_list_defined() const | core::scoring::methods::EnergyMethodOptions | |
| nmer_svm_list_defined_ | core::scoring::methods::EnergyMethodOptions | private |
| nmer_svm_pssm_feat() const | core::scoring::methods::EnergyMethodOptions | |
| nmer_svm_pssm_feat(bool const setting) | core::scoring::methods::EnergyMethodOptions | |
| nmer_svm_pssm_feat_ | core::scoring::methods::EnergyMethodOptions | private |
| nmer_svm_rank() const | core::scoring::methods::EnergyMethodOptions | |
| nmer_svm_rank(std::string const &filename) | core::scoring::methods::EnergyMethodOptions | |
| nmer_svm_rank_ | core::scoring::methods::EnergyMethodOptions | private |
| nmer_svm_rank_defined() const | core::scoring::methods::EnergyMethodOptions | |
| nmer_svm_rank_defined_ | core::scoring::methods::EnergyMethodOptions | private |
| nmer_svm_rank_list() const | core::scoring::methods::EnergyMethodOptions | |
| nmer_svm_rank_list(std::string const &filename) | core::scoring::methods::EnergyMethodOptions | |
| nmer_svm_rank_list_ | core::scoring::methods::EnergyMethodOptions | private |
| nmer_svm_rank_list_defined() const | core::scoring::methods::EnergyMethodOptions | |
| nmer_svm_rank_list_defined_ | core::scoring::methods::EnergyMethodOptions | private |
| nmer_svm_scorecut() const | core::scoring::methods::EnergyMethodOptions | |
| nmer_svm_scorecut(core::Real const &setting) | core::scoring::methods::EnergyMethodOptions | |
| nmer_svm_scorecut_ | core::scoring::methods::EnergyMethodOptions | private |
| nmer_svm_scorecut_defined() const | core::scoring::methods::EnergyMethodOptions | |
| nmer_svm_scorecut_defined_ | core::scoring::methods::EnergyMethodOptions | private |
| nmer_svm_term_length() const | core::scoring::methods::EnergyMethodOptions | |
| nmer_svm_term_length(core::Size const setting) | core::scoring::methods::EnergyMethodOptions | |
| nmer_svm_term_length_ | core::scoring::methods::EnergyMethodOptions | private |
| operator!=(EnergyMethodOptions const &a, EnergyMethodOptions const &b) | core::scoring::methods::EnergyMethodOptions | friend |
| operator=(EnergyMethodOptions const &src) | core::scoring::methods::EnergyMethodOptions | |
| operator==(EnergyMethodOptions const &a, EnergyMethodOptions const &b) | core::scoring::methods::EnergyMethodOptions | friend |
| ordered_pt_wat_penalty() const | core::scoring::methods::EnergyMethodOptions | |
| ordered_pt_wat_penalty_ | core::scoring::methods::EnergyMethodOptions | private |
| ordered_wat_penalty() const | core::scoring::methods::EnergyMethodOptions | |
| ordered_wat_penalty_ | core::scoring::methods::EnergyMethodOptions | private |
| pb_bound_tag() const | core::scoring::methods::EnergyMethodOptions | |
| pb_bound_tag() | core::scoring::methods::EnergyMethodOptions | |
| pb_bound_tag(std::string const &tag) | core::scoring::methods::EnergyMethodOptions | |
| pb_bound_tag_ | core::scoring::methods::EnergyMethodOptions | private |
| pb_unbound_tag() const | core::scoring::methods::EnergyMethodOptions | |
| pb_unbound_tag() | core::scoring::methods::EnergyMethodOptions | |
| pb_unbound_tag(std::string const &tag) | core::scoring::methods::EnergyMethodOptions | |
| pb_unbound_tag_ | core::scoring::methods::EnergyMethodOptions | private |
| protein_dielectric() const | core::scoring::methods::EnergyMethodOptions | |
| protein_dielectric(Real setting) | core::scoring::methods::EnergyMethodOptions | |
| protein_dielectric_ | core::scoring::methods::EnergyMethodOptions | private |
| put_intra_into_total() const | core::scoring::methods::EnergyMethodOptions | |
| put_intra_into_total(bool const setting) | core::scoring::methods::EnergyMethodOptions | |
| put_intra_into_total_ | core::scoring::methods::EnergyMethodOptions | private |
| rna_options() const | core::scoring::methods::EnergyMethodOptions | |
| rna_options() | core::scoring::methods::EnergyMethodOptions | |
| rna_options(rna::RNA_EnergyMethodOptions const &opts) | core::scoring::methods::EnergyMethodOptions | |
| rna_options_ | core::scoring::methods::EnergyMethodOptions | private |
| secondary_structure_weights() const | core::scoring::methods::EnergyMethodOptions | |
| secondary_structure_weights() | core::scoring::methods::EnergyMethodOptions | |
| set_aa_composition_setup_files(utility::vector1< std::string > const &input_filenames) | core::scoring::methods::EnergyMethodOptions | inline |
| set_cartesian_bonded_linear(bool lin_in) | core::scoring::methods::EnergyMethodOptions | inline |
| set_cartesian_bonded_parameters(Real len, Real ang, Real tors, Real proton, Real imp) | core::scoring::methods::EnergyMethodOptions | inline |
| set_cartesian_bonded_skip_cutpoints(bool setting) | core::scoring::methods::EnergyMethodOptions | inline |
| set_density_sc_scale_byres(core::Real newscscale) | core::scoring::methods::EnergyMethodOptions | |
| set_density_sc_scale_byres(core::chemical::AA aa, core::Real newscscale) | core::scoring::methods::EnergyMethodOptions | |
| set_elec_sigmoidal_die_params(Real D, Real D0, Real S) | core::scoring::methods::EnergyMethodOptions | |
| set_method_weights(ScoreType const &type, utility::vector1< Real > const &wts) | core::scoring::methods::EnergyMethodOptions | |
| set_mhc_epitope_setup_files(utility::vector1< std::string > const &input_filenames) | core::scoring::methods::EnergyMethodOptions | inline |
| set_netcharge_setup_files(utility::vector1< std::string > const &input_filenames) | core::scoring::methods::EnergyMethodOptions | inline |
| set_strand_strand_weights(int ss_lowstrand, int ss_cutoff) | core::scoring::methods::EnergyMethodOptions | |
| show(std::ostream &out) const | core::scoring::methods::EnergyMethodOptions | |
| smooth_fa_elec() const | core::scoring::methods::EnergyMethodOptions | |
| smooth_fa_elec(bool setting) | core::scoring::methods::EnergyMethodOptions | |
| smooth_fa_elec_ | core::scoring::methods::EnergyMethodOptions | private |
| split_unfolded_label_type() const | core::scoring::methods::EnergyMethodOptions | |
| split_unfolded_label_type(std::string const &label_type) | core::scoring::methods::EnergyMethodOptions | |
| split_unfolded_label_type_ | core::scoring::methods::EnergyMethodOptions | private |
| split_unfolded_value_type() const | core::scoring::methods::EnergyMethodOptions | |
| split_unfolded_value_type(std::string const &value_type) | core::scoring::methods::EnergyMethodOptions | |
| split_unfolded_value_type_ | core::scoring::methods::EnergyMethodOptions | private |
| ss_weights_ | core::scoring::methods::EnergyMethodOptions | private |
| symmetric_gly_tables() const | core::scoring::methods::EnergyMethodOptions | |
| symmetric_gly_tables(bool const setting) | core::scoring::methods::EnergyMethodOptions | |
| symmetric_gly_tables_ | core::scoring::methods::EnergyMethodOptions | private |
| target_clash_pdb(std::string const &setting) | core::scoring::methods::EnergyMethodOptions | |
| target_clash_pdb() const | core::scoring::methods::EnergyMethodOptions | |
| target_clash_pdb_ | core::scoring::methods::EnergyMethodOptions | private |
| unfolded_energies_type() const | core::scoring::methods::EnergyMethodOptions | |
| unfolded_energies_type(std::string const &type) | core::scoring::methods::EnergyMethodOptions | |
| unfolded_energies_type_ | core::scoring::methods::EnergyMethodOptions | private |
| use_gen_kirkwood() const | core::scoring::methods::EnergyMethodOptions | |
| use_gen_kirkwood(bool setting) | core::scoring::methods::EnergyMethodOptions | |
| use_gen_kirkwood_ | core::scoring::methods::EnergyMethodOptions | private |
| use_polarization() const | core::scoring::methods::EnergyMethodOptions | |
| use_polarization(bool setting) | core::scoring::methods::EnergyMethodOptions | |
| use_polarization_ | core::scoring::methods::EnergyMethodOptions | private |
| voids_penalty_energy_cone_distance_cutoff() const | core::scoring::methods::EnergyMethodOptions | |
| voids_penalty_energy_cone_distance_cutoff(core::Real const &setting) | core::scoring::methods::EnergyMethodOptions | |
| voids_penalty_energy_cone_distance_cutoff_ | core::scoring::methods::EnergyMethodOptions | private |
| voids_penalty_energy_cone_dotproduct_cutoff() const | core::scoring::methods::EnergyMethodOptions | |
| voids_penalty_energy_cone_dotproduct_cutoff(core::Real const &setting) | core::scoring::methods::EnergyMethodOptions | |
| voids_penalty_energy_cone_dotproduct_cutoff_ | core::scoring::methods::EnergyMethodOptions | private |
| voids_penalty_energy_containing_cones_cutoff() const | core::scoring::methods::EnergyMethodOptions | |
| voids_penalty_energy_containing_cones_cutoff(core::Size const setting) | core::scoring::methods::EnergyMethodOptions | |
| voids_penalty_energy_containing_cones_cutoff_ | core::scoring::methods::EnergyMethodOptions | private |
| voids_penalty_energy_disabled_except_during_packing() const | core::scoring::methods::EnergyMethodOptions | |
| voids_penalty_energy_disabled_except_during_packing(bool const setting) | core::scoring::methods::EnergyMethodOptions | |
| voids_penalty_energy_disabled_except_during_packing_ | core::scoring::methods::EnergyMethodOptions | private |
| voids_penalty_energy_voxel_grid_padding() const | core::scoring::methods::EnergyMethodOptions | |
| voids_penalty_energy_voxel_grid_padding(core::Real const &setting) | core::scoring::methods::EnergyMethodOptions | |
| voids_penalty_energy_voxel_grid_padding_ | core::scoring::methods::EnergyMethodOptions | private |
| voids_penalty_energy_voxel_size() const | core::scoring::methods::EnergyMethodOptions | |
| voids_penalty_energy_voxel_size(core::Real const &setting) | core::scoring::methods::EnergyMethodOptions | |
| voids_penalty_energy_voxel_size_ | core::scoring::methods::EnergyMethodOptions | private |
| water_dielectric() const | core::scoring::methods::EnergyMethodOptions | |
| water_dielectric(Real setting) | core::scoring::methods::EnergyMethodOptions | |
| water_dielectric_ | core::scoring::methods::EnergyMethodOptions | private |
| write_score_function_method_options_table_schema(utility::sql_database::sessionOP db_session) | core::scoring::methods::EnergyMethodOptions | static |
| ~EnergyMethodOptions() override | core::scoring::methods::EnergyMethodOptions | |
1.8.7